green leaf volatile biosynthesis pathway

[cmungall]

Carried from #16018.

currently this is an only-child, which is a "bad smell" (though cut grass smells nice...)

     is_a GO:0006631 ! fatty acid metabolic process
      is_a GO:0019372 ! lipoxygenase pathway *** 
       is_a GO:0010597 ! green leaf volatile biosynthetic process

not much here:

id: GO:0019372
name: lipoxygenase pathway
namespace: biological_process
def: "The chemical reactions and pathways by which an unsaturated fatty acid (such as arachidonic acid or linolenic acid) is converted to other compounds, and in which the first step is hydroperoxide formation catalyzed by lipoxygenase." [GOC:mah, PMID:17163881]
is_a: GO:0006631 ! fatty acid metabolic process
is_a: GO:0006690 ! icosanoid metabolic process

id: GO:0010597
name: green leaf volatile biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of volatile molecules emitted from green plants, such as hexenal, hexenol and hexenyl acetate, from linoleic acid or linolenic acid." [PMID:17163881]
is_a: GO:0019372 ! lipoxygenase pathway

• [ ] taxon constraints. Not sure we can assume this always happens in a leaf? If not, add a TC direct to this class rather than inheriting from PO
• [ ] xrefs, should one of these be xreffed to https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5433 @hdrabkin @tberardini
• [ ] syns. Add syns like GLV biosynthesis, GLV pathway
• [ ] add has-parts?
• [ ] chemical entity. Is GLV a valid CHEBI request, or is it a grouping?
• [ ] add more specific classes? E.g (Z)-3-hexen-1-yl acetate
• [ ] add an axiom to response to stress?
• [ ] text defs: these don't really mirror each other, ideally we would refine a parent class with differentiae

[hdrabkin]

????!!!!! 8-( First off, I'd change term name to green plant ... and not green leaf?

[hdrabkin]

Collecting supporting info for this term PMID:17163881, maybe the term "acetyl CoA:(Z)-3-hexen-1-ol acetyltransferase activity" should have a relation to this process? Any other 'zymes" ?? @tberardini can you send me a full copy of the PMID (I have no subscription to the journal)

[hdrabkin]

Note, the PMID for acetyl CoA:(Z)-3-hexen-1-ol acetyltransferase activity is listed as PMID:17163883 however, it goes go Franzén LE, Schultz GS. Transforming growth factor-beta enhances connective tissue repair in perforated rat mesentery but not peritoneal macrophage chemotaxis. Wound Repair Regen. 1993 Jul;1(3):149-55. PubMed PMID: 17163883. But tair uses PMID:17163881 in annotation to this , which goes to a more reasonable paper (Plant J); this will be fixed..

[cmungall]

green leaf volatile is the name in the literature.

good catch on the PMID, wonder how many of these we have

[tberardini]

@hdrabkin PMID:29472638 = Nat Rev Drug Discov. 2018 May;17(5):317-332. doi: 10.1038/nrd.2018.14. Epub 2018 Mar 23. Unexplored therapeutic opportunities in the human genome.

Is that really the paper you want?

[tberardini]

Here's a PMC paper:

Green Leaf Volatiles: A Plant’s Multifunctional Weapon against Herbivores and Pathogens https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794753/

and an older one

Green leaf volatiles: hydroperoxide lyase pathway of oxylipin metabolism. https://www.ncbi.nlm.nih.gov/pubmed/16595187

Green leaf volatiles (GLVs) are C(6) aldehydes, alcohols, and their esters formed through the hydroperoxide lyase pathway of oxylipin metabolism.

[hdrabkin]

No @tberardini , it was this one: PMID:17163881

Copy paste buffer did not clear. This is the PMID used for the def

[tberardini]

@hdrabkin Sent.

[tberardini]

@hdrabkin Do you need anything else from me? If not, I will unassign myself from this issue but will keep monitoring.

[hdrabkin]

What exactly needs to be done here? What did you do? DO I need to add synonyms, etc.?

[cmungall]

see my checklist at the top

[tberardini]

I didn't do anything on the checklist, but in November, I sent the copy of the paper that you requested and provided a couple of additional references I found that could be helpful.

[hdrabkin]

Oh right, I see I have them; I'll take a look this weekend (but I am clearly not an expert at all on this branch of plant biochemistry).

[ValWood]

my notes from another ticket: GO:0010597 green leaf volatile biosynthetic process Definition The chemical reactions and pathways resulting in the formation of volatile molecules emitted from green plants, such as hexenal, hexenol and hexenyl acetate, from linoleic acid or linolenic acid. PMID:17163881

This term is positioned under GO:0019372 lipoxygenase pathway

Definition (GO:0019372 GONUTS page) The chemical reactions and pathways by which an unsaturated fatty acid (such as arachidonic acid or linolenic acid) is converted to other compounds, and in which the first step is hydroperoxide formation catalyzed by lipoxygenase. PMID:17163881

which must be narrower than 'green leaf volatile'

Most annotations are IMP (maybe a readout for leaf wounding?)